[QE-users] [SPAM] Re: Re: Blue moon ensemble calculations in quantum espresso

Wed Dec 14 18:37:01 CET 2022

Dear Paolo,

Thanks for letting me know. Just asking for future reference, are there any plans to add support for it again in the future, or to include meta-dynamics within the QE code itself?

Thanks and regards,
Payal

[https://ucomm.unl.edu/images/email-signature/Nebraska_N_RGB_small_on_white.gif]

Payal Chaudhary

Graduate Research Asst

University of Nebraska–Lincoln

Chemical & Biomolecular Engineering

212 Othmer Hall, Lincoln, NE 68588

________________________________
From: Paolo Giannozzi <paolo.giannozzi at uniud.it>
Sent: Wednesday, December 14, 2022 2:58 AM
To: Payal Chaudhary <pchaudhary3 at huskers.unl.edu>
Subject: Re: [QE-users] [SPAM] Re: Blue moon ensemble calculations in quantum espresso

Non-NU Email

On 12/14/22 00:54, Payal Chaudhary wrote:

> Thank you for the resources, they're very helpful. I didn't know that
> PLUMED can be used with newer versions of Quantum Espresso

unfortunately it can't. Support for the old version (v.1.3) of PLUMED
has been present for a long time but it was recently removed.

Paolo

> Payal
>
>
>
>
> *Payal Chaudhary*
>
> Graduate Research Asst
>
> University of Nebraska–Lincoln
>
> Chemical & Biomolecular Engineering
>
> 212 Othmer Hall, Lincoln, NE 68588
>
> ------------------------------------------------------------------------
> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of
> Giovanni La Penna <giovanni.lapenna at cnr.it>
> *Sent:* Tuesday, December 13, 2022 5:29 AM
> *To:* Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> *Subject:* Re: [QE-users] Blue moon ensemble calculations in quantum
> espresso
> Non-NU Email
>
> Payal,
>
> It is possible to use QE with PLUMED and then to apply PLUMED recipes:
>
> https://urldefense.com/v3/__https://www.plumed.org__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZaD6B9R9$ <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fwww.plumed.org__*3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZaD6B9R9*24&data=05*7C01*7Cpaolo.giannozzi*40uniud.it*7C2818eb7c95d04c0e589808dadd657cb5*7C6e6ade15296c4224ac581c8ec2fd53a8*7C0*7C0*7C638065725221086498*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=plS7R*2BhPY79AJkWW651eO8CDSVlg60MLn8a8kRf2bKM*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zMFrjAK7g$ >
>
> Recently blue-moon sampling has been done with PLUMED combined together
> with other DFT codes:
>
> https://urldefense.com/v3/__https://doi.org/10.1007/s11244-021-01516-y__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZT1t97kW$ <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fdoi.org*2F10.1007*2Fs11244-021-01516-y__*3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZT1t97kW*24&data=05*7C01*7Cpaolo.giannozzi*40uniud.it*7C2818eb7c95d04c0e589808dadd657cb5*7C6e6ade15296c4224ac581c8ec2fd53a8*7C0*7C0*7C638065725221086498*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=tlOvtHSuWGkUd*2BaQXLzCCNTtATDIYsw*2FA4PDBvqpF5o*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zP3lar9KA$ >
>
> The last time I used PLUMED 1.x in QE 5.2 (2016) to perform manipulations
> (not properly a correct sampling):
>
> https://urldefense.com/v3/__https://doi.org/10.3390/molecules23123308__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZbQEGTUz$ <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fdoi.org*2F10.3390*2Fmolecules23123308__*3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZbQEGTUz*24&data=05*7C01*7Cpaolo.giannozzi*40uniud.it*7C2818eb7c95d04c0e589808dadd657cb5*7C6e6ade15296c4224ac581c8ec2fd53a8*7C0*7C0*7C638065725221086498*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=W2M71JqvtY2Fj1amsbYkZXs8Lh30SAaUyfHwmRIxzxA*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zOvsKK3sg$ >
>
> With a little handcraft, it is possible to use PW of QE 7.0 with PLUMED
> 2.7.x.
> Unfortunately not yet CP, as far as I know.
>
> HTH,
>            Giovanni
>
> On Mon, Dec 12, 2022 at 09:59:48PM +0000, Payal Chaudhary wrote:
>> I had a question about running blue moon calculations with Quantum Espresso.
>>
>> To get the free energy profile along a reaction coordinate, we can run several constrained MD calculations and use the blue moon ensemble averages to get free energy gradients. These gradients can then be integrated to get the free energy profile. This methodology  is described in the paper "Giovanni Ciccotti & Mauro Ferrario (2004)
> Blue Moon Approach to Rare Events, Molecular Simulation, 30:11-12,
> 787-793"
> (doi<https://urldefense.com/v3/__https://doi.org/10.1080/0892702042000270214__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZasMlba_$ >)
>>
>> To calculate these averages, we need some quantities in the output file, such as the metric tensor z, and the Lagrange multiplier λ, for each time step. In the case of VASP, these can be obtained by specifying an additional input tag.
>>
>> The QE docs are not clear on whether these quantities are printed in the output, and I couldn't find any discussion on this in the forums either.
>> I would really appreciate if someone could point me in the right direction to compute blue moon ensemble averages with the QE code.
>>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
> Quantum ESPRESSO is supported by MaX
> (https://urldefense.com/v3/__http://www.max-centre.eu__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZTsfDE33$ )
> users mailing list users at lists.quantum-espresso.org
> https://urldefense.com/v3/__https://lists.quantum-espresso.org/mailman/listinfo/users__;!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZa6EQrEG$ <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Flists.quantum-espresso.org*2Fmailman*2Flistinfo*2Fusers__*3B!!PvXuogZ4sRB2p-tU!E7oPJQZU_TGV_mHpRbnDdoLZWsSwIxm7GZoDAJtJssSLWr61cSCWylv2M5wcoLaCMCp3LxQ6hliIOgtUiYcFpu1Nsb9sZa6EQrEG*24&data=05*7C01*7Cpaolo.giannozzi*40uniud.it*7C2818eb7c95d04c0e589808dadd657cb5*7C6e6ade15296c4224ac581c8ec2fd53a8*7C0*7C0*7C638065725221086498*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=HH6euzLEZWGsvfqrCknh*2F8KWiXzbtc46xdbGoSY0IHQ*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zN01kX-_A$ >
>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (https://urldefense.com/v3/__http://www.max-centre.eu__;!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zPPkq679w$ )
> users mailing list users at lists.quantum-espresso.org
> https://urldefense.com/v3/__https://lists.quantum-espresso.org/mailman/listinfo/users__;!!PvXuogZ4sRB2p-tU!FAjJY45qkL4_ja5Vp4nbGqDI-a0iPLxeCHPcL-t-BNU_9Y90tlPlbPYPnmZ7McpN_2D9ZQ_rHEoBK9j30pX_b6LPNfB29zNRCLQxwQ$

--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20221214/75464505/attachment.html>